Thanks for the advice. I already tried the SMC reset, but no good i'm afraid. It did fix crackly onboard audio though (same rMBP ><)
Well, i've been using a couple of different (Belkin and Logik) USB hubs in order to make USB audio devices work. There is a thread here regarding that somewhere. It seems that using these hubs drops the ports down to USB 2 and for some reason that solves the issue. It also solves the hard disk eject problem being discussed here.
What is new though, as far as I can tell, is that now I have had a chance to test the variety of USB problems with my rMBP again, it seems that since I last checked the USB audio problem has gone. This could have been the firmware update that came around April, or Mountain Lion 10.8.3. I have installed both since that time.
However, minus hubs, the HD eject problem on the right hand port remains. I wonder if new rMBPs still suffer from this. If so, would it be worth looking for a replacement under Applecare... I wonder.
FYI: G-Technology G-Safe drive ejecting today. However G-Raid, on USB, working fine. (though the G-Safe is dreadful in many ways)